I have had half doors and soft windows on my Jeep since I got it 8 years ago. I've replaced the soft windows twice because the plastic got too scratched or a zipper broke. The key is keeping the windows clean with a wet towel and never rubbing the dirt into the plastic. They seal perfectly.
Half doors are the best option offroad IMO because they let you lean to see more in front of you while keeping you in the Jeep. The upper plastic windows are awesome because they open and close easily and give you a way better opening than the sliders. I use a binder clip to hold the plastic window if I want to open it only half way, which adds some versatility.
A pair of new soft windows can be had for about $75 on eBay.